Here is a link to a list of hundreds of websites for Middle School Students:

http://gws.ala.org/level/appropriate-middle-school-aged-youth?page=1

Here are some more websites:

CryptoKids - Learn to Make and Break Codes like Secret OPS: http://www.nsa.gov/kids/home.shtml

The Artist's ToolKit - Create art like an artist - http://www.artsconnected.org/toolkit/explore.cfm

BrainPOP - Fun games and information - http://www.brainpop.com/

Building Big - Explore large structures and what it takes to build them with BUILDING BIG - http://www.pbs.org/wgbh/buildingbig/index.html

Cool Math Games - http://www.coolmath-games.com/